Aptamer–protein interactions: from regulation to biomolecular detection

C Ji, J Wei, L Zhang, X Hou, J Tan, Q Yuan… - Chemical …, 2023‏ - ACS Publications
Serving as the basis of cell life, interactions between nucleic acids and proteins play
essential roles in fundamental cellular processes. Aptamers are unique single-stranded …

Critical assessment of methods for predicting the 3D structure of proteins and protein complexes

SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023‏ - annualreviews.org
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

TC Terwilliger, D Liebschner, TI Croll, CJ Williams… - Nature …, 2024‏ - nature.com
Artificial intelligence-based protein structure prediction methods such as AlphaFold have
revolutionized structural biology. The accuracies of these predictions vary, however, and …

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning

K Stahl, A Graziadei, T Dau, O Brock… - Nature …, 2023‏ - nature.com
While AlphaFold2 can predict accurate protein structures from the primary sequence,
challenges remain for proteins that undergo conformational changes or for which few …

UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER

PA DaRosa, I Penchev, SC Gumbin, F Scavone… - Nature, 2024‏ - nature.com
Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is
widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that …

Structural basis for clearing of ribosome collisions by the RQT complex

K Best, K Ikeuchi, L Kater, D Best, J Musial… - Nature …, 2023‏ - nature.com
Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in
ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress …

Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning

X Peng, Y Lei, P Feng, L Jia, J Ma, D Zhao… - Nature machine …, 2023‏ - nature.com
Computational modelling of the interactions between T-cell receptors (TCRs) and epitopes
is of great importance for immunotherapy and antigen discovery. However, current TCR …

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

MF Lensink, G Brysbaert, N Raouraoua… - Proteins: Structure …, 2023‏ - Wiley Online Library
We present the results for CAPRI Round 54, the 5th joint CASP‐CAPRI protein assembly
prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo …

Deep learning for the PSIPRED protein analysis workbench

DWA Buchan, L Moffat, A Lau… - Nucleic Acids …, 2024‏ - academic.oup.com
The PSIRED Workbench is a long established and popular bioinformatics web service
offering a wide range of machine learning based analyses for characterizing protein …

Identification of type VI secretion system effector-immunity pairs using structural bioinformatics

AM Geller, M Shalom, D Zlotkin, N Blum… - Molecular Systems …, 2024‏ - embopress.org
The type VI secretion system (T6SS) is an important mediator of microbe–microbe and
microbe–host interactions. Gram-negative bacteria use the T6SS to inject T6SS effectors …